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Status |
Public on Feb 24, 2021 |
Title |
DMSO_TAM_A |
Sample type |
SRA |
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Source name |
DMSO_TAM
|
Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6 genotype/variation: Mutant RNF40RosaCreERT2 mouse cell type: Primary Calvarial Osteoblasts treatment: for 7 d with 250nM 4-hydroxytamoxifen, and then for additional 7 days with DMSO library prep kit: TruSeq RNA Smaple Prep Kit-v2, Illumina
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Treatment protocol |
For induction of RNF40 knockout, the cells were treated with 250nM of 4-hydroxytamoxifen or equivalent volume of vehicle (ethanol). For differentiation, cells were treated with 5 mM β-glycerophosphate and 0.2 mM ascorbate. For vitamin D studies, cells were treated for 7 days with 10nM calcitriol or equal volume of vehicle (DMSO).
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Growth protocol |
Mouse calvarial osteoblasts were maintained in aMEM complete media with 10% FBS and 1% P/S
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Extracted molecule |
total RNA |
Extraction protocol |
The total cell RNA was isolated with standard TRIzol extraction protocol 4 µg of total cell RNA was used for library preparation with NEXTflex Rapid Directional mRNA-Seq from Bioo Scientific and 500ng of total cell RNA was used for library preparation with TruSeq RNA Smaple Prep Kit-v2 following manufacturers' protocols.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
The FASTQ files were mapped to the mouse mm9 genome using TopHat Gapped-read mapper for RNA-seq data with very-sensitive BOWTIE2 settings. The differential analysis was performed by using Cuffdiff with default settings. Genome_build: mm9 Supplementary_files_format_and_content: The provided mRNA-Seq analysis files present the differentially regulated genes between the indicated conditions in excel file format.
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Submission date |
Aug 09, 2019 |
Last update date |
Feb 24, 2021 |
Contact name |
Steven A. Johnsen |
Organization name |
Robert Bosch Center for Tumor Diseases
|
Lab |
Molecular Cancer Epigenetics
|
Street address |
Auerbachstraße 112
|
City |
Stuttgart |
State/province |
BW |
ZIP/Postal code |
70376 |
Country |
Germany |
|
|
Platform ID |
GPL21103 |
Series (2) |
GSE135628 |
RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk [RNA-seq] |
GSE135629 |
RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk |
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Relations |
BioSample |
SAMN12542666 |
SRA |
SRX6686951 |